I've thought about this question before, and I agree with the general consensus here. I've only fished Penns half a dozen times, little j over a hundred, but I would still vote Penns for the following reasons:
Remoteness/scenery: Penns by far
Overall challenge and puzzles to figure out presented to fisherman: Penns by far, but your hair might be gone by the time you leave.
Diversity of wildlife that you may run into: Penns
Diversity and overall quality of hatches: Penns by far, though I feel the diversity is starting to return in the lj.
Best chance of 20"+ brown: Probably Penns, but I think theres a lot more big trout (a few over 25") in the lj than most people think. I think they're just really tough to catch for a variety of reasons.
Where to catch the most fish (most of the time): lj for sure
Fishability throughout the year (temp wise): lj
Best chance of relative solitude during prime hatch season: don't really know, used to be lj but it gets worse every year.
Overall consistency of good dry fly water: Probably Penns
Overall consistency of good wet fly water: don't really know, both are good, I would lean Penns
Overall consistency of good nymphing water: lj by far imo
Overall consistency of good terrestrial fishing (assuming good temps): don't really know, but lj hasn't been good for me the last few years.
This is only my opinion, and I'm sure I'm missing stuff.